It is important to distinguish two ways that "materialism" is used. One is in science, which is described as a "materialist" enterprise, focusing on matter and energy and their interactions. Modern science operates under a rule of methodological materialism that limits it to attempting to explain the natural world using natural -- matter and energy -- causes. Science in and of itself is neutral to religion: by definition, it lacks the ability to hold constant supernatural forces. It is neither antireligious nor pro-religious: it is neutral because supernatural forces are outside of what it can consider as causation. MEs go beyond the methodological materialism of science to propose that the laws of nature are all there is: the supernatural does not exist. This is a form of philosophical materialism (naturalism or scientism), which is distinct from the practical rules of how to do science.
That is to say: A totally material (or physical or natural) view of the universe can never be proved through science. There will always be gaps in our knowledge. However, in terms of trying to explain individual phenomina, the material explaination is the only one that science can touch on.
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